Fig. 2: Model interpretability and cross-tissue signatures of cell potency.
From: Improved reconstruction of single-cell developmental potential with CytoTRACE 2
a, Schematic for characterizing CytoTRACE 2 gene sets and feature importance. b, UMAP of gene set expression levels in training–test sets, aggregated in a 0.5 × 0.5 grid, colored by CytoTRACE 2 (top) or ground truth potency (bottom). c, Expression of top 500 positive (pos.) and negative (neg.) markers per potency category, shown across 237 pseudo-bulks aggregated by phenotype, species and platform from training–test sets. d, Overview of a CRISPR knockout (KO) screen assessing in vivo differentiation effects in hematopoietic stem cells (HSCs)38. e, Enrichment of top CytoTRACE 2 multipotency markers among genes whose knockout promotes or inhibits HSC differentiation (from d), using GSEA. f, GSEA of 537 pathways in genes ranked by multipotency scores, highlighting ‘cholesterol metabolism’. g, Top: overview of UFA pathways, inspired by ref. 42. Bottom: top UFA biosynthesis genes (Fads1, Fads2 and Scd2) ranked by GSEA and CytoTRACE 2 multipotency scores). h, Single-sample GSEA of UFA genes across 237 pseudo-bulk samples, colored by tissue type as in c. ****P < 0.0001 (one-sided permutation testing). Box plots show medians, quartiles and 1.5 × IQR. i, qPCR of UFA genes in FACS-purified mouse hematopoietic subsets (n = 3), normalized to HSC/MPP; Actb as internal control. MPP, multipotent progenitor; CMP, common myeloid progenitor; CLP, common lymphoid progenitor. Violin plots show median and range. j, In situ mRNA imaging of mouse jejunum (top) shows spatial expression of multipotent (Lgr5 and Fgfbp1), proliferation (Mki67), and UFA (Fads1, Fads2 and Scd2) marker genes in crypts and villi. Higher magnification views (bottom) highlight boxed regions. Cell boundaries were visualized with E-cadherin immunostaining; asterisks mark representative Lgr5+ crypt base columnar (CBC) cells. TA, transit-amplifying. Scale bars, 50 μm (top), 10 μm (bottom). Images are representative of three mice. Images in a, d, g, i, j were created using BioRender.com. NES, normalized enrichment score.
